Protein Unfolding and Disordered Proteins

IDP Force Field Development
Intrinsically disordered proteins (IDPs) are notoriously challenging to study both experimentally and computationally. Our findings highlight how IDPs, with their rugged energy landscapes, are highly sensitive test systems that are capable of revealing force field deficiencies and, therefore, contributing to force field development.
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SESCA: Semi-Empirical-Spectrum-Calculation-Algorithm
SESCA is a computational method that allows rapid and accurate prediction of CD spectra from three-dimensional protein model structures. Calculations allow a direct comparison between the measured CD spectrum of a target protein and the predicted CD spectra based on model structures or structural ensembles to determine the model quality.
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<h1>Tension Induced Titin Kinase Activation</h1>
Activation of the titin kinase, the catalytic domain of the muscle protein titin, requires major conformational rearrangements resulting in the exposure of its phosphorylation site. Force probe MD simulations can give a detailed description of the activation mechanism and can test the hypothesis that it is the force sensor for the muscle cell.
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In virtually every biochemistry lab, urea is used as protein denaturant. However, despite its ubiquiteous use, only little is known about the molecular mechanism underlying urea-induced protein denaturation.To study structure and energetics of aqueous urea solutions, we have carried out molecular dynamics (MD) simulations.
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Nanomechanical devices or molecular machines will, for a broad range of applications, most likely be powered by light or other kinds of electromagnetic radiation. The major reasons are ease of addressability, picosecond reaction times to external stimuli, and compatibility with a broad range of ambient substances, such as solvents, electrolytes, or gases.
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Proteins enable living organisms to move, metabolize and sense, in short, to function. To fulfill such diverse tasks, proteins take up a specific fold, their native structure.The factors driving the complex folding process are not yet fully understood. [more]
Some proteins such as the Cold Shock protein Bc-CsP are not strongly affected by the presence of urea in molecular dynamics (MD) simulations within reachable simulation times. To study urea-induced unfolding for the Cold Shock protein, we generate partially unfolded states by high-temperature unfolding and simulate these at different conditions.
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